Package org.openscience.cdk.protein.data
Class PDBStrand
- java.lang.Object
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- org.openscience.cdk.ChemObject
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- org.openscience.cdk.AtomContainer
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- org.openscience.cdk.Strand
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- org.openscience.cdk.protein.data.PDBStrand
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- All Implemented Interfaces:
Serializable
,Cloneable
,IAtomContainer
,ICDKObject
,IChemObject
,IChemObjectListener
,IStrand
public class PDBStrand extends Strand
An entry in the PDB database. It is not just a regular protein, but the regular PDB mix of protein or protein complexes, ligands, water molecules and other species.- Author:
- Egon Willighagen
- See Also:
- Serialized Form
- Source code:
- main
- Belongs to CDK module:
- pdb
- Keywords:
- polymer
- Created on:
- 2006-04-19
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Field Summary
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Fields inherited from interface org.openscience.cdk.interfaces.IChemObject
ALIPHATIC, AROMATIC, CONJUGATED, HYDROGEN_BOND_ACCEPTOR, HYDROGEN_BOND_DONOR, IN_RING, MAPPED, NOT_IN_RING, PLACED, REACTIVE_CENTER, SINGLE_OR_DOUBLE, TYPEABLE, VISITED
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Constructor Summary
Constructors Constructor Description PDBStrand()
Constructs a new Polymer to store the Monomers.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addAtom(IAtom oAtom, IMonomer oMonomer)
Adds the atom oAtom to a specified Monomer.Collection<String>
getMonomerNamesInSequentialOrder()
Returns the monomer names in the order in which they were added.String
toString()
Returns a one line description of this IChemObject.-
Methods inherited from class org.openscience.cdk.Strand
addAtom, clone, getMonomer, getMonomerCount, getMonomerNames, getMonomers, getStrandName, getStrandType, removeMonomer, setStrandName, setStrandType
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Methods inherited from class org.openscience.cdk.AtomContainer
add, addBond, addBond, addBond, addElectronContainer, addLonePair, addLonePair, addSingleElectron, addSingleElectron, addStereoElement, atoms, bonds, contains, contains, contains, contains, contains, electronContainers, getAtom, getAtomCount, getAtomNumber, getBond, getBond, getBondCount, getBondNumber, getBondNumber, getBondOrderSum, getConnectedAtomsCount, getConnectedAtomsList, getConnectedBondsCount, getConnectedBondsCount, getConnectedBondsList, getConnectedElectronContainersList, getConnectedLonePairsCount, getConnectedLonePairsList, getConnectedSingleElectronsCount, getConnectedSingleElectronsList, getElectronContainer, getElectronContainerCount, getFirstAtom, getLastAtom, getLonePair, getLonePairCount, getLonePairNumber, getMaximumBondOrder, getMinimumBondOrder, getSingleElectron, getSingleElectronCount, getSingleElectronNumber, getTitle, indexOf, indexOf, indexOf, indexOf, isEmpty, lonePairs, newAtom, newAtom, newBond, remove, removeAllBonds, removeAllElectronContainers, removeAllElements, removeAtom, removeAtom, removeAtomAndConnectedElectronContainers, removeAtomOnly, removeAtomOnly, removeBond, removeBond, removeBond, removeElectronContainer, removeElectronContainer, removeLonePair, removeLonePair, removeSingleElectron, removeSingleElectron, setAtom, setAtoms, setBonds, setStereoElements, setTitle, shallowCopy, singleElectrons, stateChanged, stereoElements
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Methods inherited from class org.openscience.cdk.ChemObject
addListener, addProperties, clear, compare, flags, getBuilder, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, is, notifyChanged, notifyChanged, removeListener, removeProperty, set, setFlag, setFlags, setID, setNotification, setProperties, setProperty
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Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
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Methods inherited from interface org.openscience.cdk.interfaces.IAtomContainer
add, addBond, addBond, addBond, addElectronContainer, addLonePair, addLonePair, addSingleElectron, addSingleElectron, addStereoElement, atoms, bonds, contains, contains, contains, contains, contains, electronContainers, getAtom, getAtomCount, getAtomNumber, getBond, getBond, getBondCount, getBondNumber, getBondNumber, getBondOrderSum, getConnectedAtomsCount, getConnectedAtomsList, getConnectedBondsCount, getConnectedBondsCount, getConnectedBondsList, getConnectedElectronContainersList, getConnectedLonePairsCount, getConnectedLonePairsList, getConnectedSingleElectronsCount, getConnectedSingleElectronsList, getElectronContainer, getElectronContainerCount, getFirstAtom, getLastAtom, getLonePair, getLonePairCount, getLonePairNumber, getMaximumBondOrder, getMinimumBondOrder, getSingleElectron, getSingleElectronCount, getSingleElectronNumber, getTitle, indexOf, indexOf, indexOf, indexOf, isEmpty, lonePairs, newAtom, newAtom, newAtom, newAtom, newBond, newBond, remove, removeAllBonds, removeAllElectronContainers, removeAllElements, removeAtom, removeAtom, removeAtomAndConnectedElectronContainers, removeAtomOnly, removeAtomOnly, removeBond, removeBond, removeBond, removeElectronContainer, removeElectronContainer, removeLonePair, removeLonePair, removeSingleElectron, removeSingleElectron, setAtom, setAtoms, setBonds, setStereoElements, setTitle, singleElectrons, stereoElements
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Methods inherited from interface org.openscience.cdk.interfaces.ICDKObject
getBuilder
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Methods inherited from interface org.openscience.cdk.interfaces.IChemObject
addListener, addProperties, clear, flags, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, is, notifyChanged, notifyChanged, removeListener, removeProperty, set, setFlag, setFlags, setID, setNotification, setProperties, setProperty
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Methods inherited from interface org.openscience.cdk.interfaces.IChemObjectListener
stateChanged
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Method Detail
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addAtom
public void addAtom(IAtom oAtom, IMonomer oMonomer)
Adds the atom oAtom to a specified Monomer. Additionally, it keeps record of the iCode.
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getMonomerNamesInSequentialOrder
public Collection<String> getMonomerNamesInSequentialOrder()
Returns the monomer names in the order in which they were added.- See Also:
IPolymer.getMonomerNames()
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toString
public String toString()
Description copied from class:AtomContainer
Returns a one line description of this IChemObject.- Specified by:
toString
in interfaceIChemObject
- Overrides:
toString
in classStrand
- Returns:
- a String representation of this object
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